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US9957494B2 - Crystal structure of human four-phosphate adaptor protein 2 glycolipid transfer protein like domain - Google Patents

Crystal structure of human four-phosphate adaptor protein 2 glycolipid transfer protein like domain Download PDF

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US9957494B2
US9957494B2 US15/327,583 US201515327583A US9957494B2 US 9957494 B2 US9957494 B2 US 9957494B2 US 201515327583 A US201515327583 A US 201515327583A US 9957494 B2 US9957494 B2 US 9957494B2
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fapp2
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compound
gltp
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US20170349889A1 (en
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Muthuraman Meiyappan
Maria A. DeMatteis
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Fondazione Telethon
Takeda Pharmaceutical Co Ltd
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Fondazione Telethon
Shire Human Genetics Therapies Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2462—Lysozyme (3.2.1.17)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01017—Lysozyme (3.2.1.17)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G06F19/12—
    • G06F19/16—
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/20—Protein or domain folding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2299/00—Coordinates from 3D structures of peptides, e.g. proteins or enzymes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • This invention relates to the provision of a high resolution crystal structure of the human four-phosphate adaptor protein 2 (FAPP2) glycolipid transfer protein (GLTP) like domain and the use of this structure in drug discovery.
  • FAPP2 human four-phosphate adaptor protein 2
  • GLTP glycolipid transfer protein
  • Fabry disease (sometimes also called Anderson-Fabry disease) is a rare X-linked disorder characterized by the absence of ⁇ -galactosidase A ( ⁇ -Gal A), an enzyme required for the normal processing of glycosphingolipids in mammalian lysosomes.
  • ⁇ -Gal A ⁇ -galactosidase A
  • the loss of ⁇ -Gal A leads to accumulation of the neutral globotriaosylceramide (Gb3), also known as ceramide trihexoside (CTH), within the heart, kidney, liver, and vascular endothelial cells. Renal and cardiac diseases are the most common cause of mortality and morbidity in Fabry patients [1, 2].
  • Hemizygous males, homozygous females, and some heterozygous females experience progressive organ dysfunction manifesting clinically as angiokeratomas, acroparathesis, stroke, cardiomyopathies, myocardian infarction and renal failure [1].
  • the kidney is exceptionally susceptible to damage from Gb3 deposition with several published reports of glycosphingolipid localized to the podocytes, vascular endothelial cells, and epithelial cells of the glomerulus. Loss of podocytes by apoptosis leads to glomerulosclerosis and drastically reduced kidney function. Affected individuals vary in disease progression and severity of symptoms.
  • Fabry disease Historically, treatment options for Fabry patients were limited to symptomatic relief of renal and cardiovascular complications [3]. Attempts at more severe treatments, namely organ transplantation [4,5] and plasmapheresis [6], did not prove successful.
  • ERT enzyme replacement therapy
  • agalsidase alfa Replagal®, TKT/Shire
  • agalsidase beta Fabrazyme®, Genzyme
  • ERT enzyme replacement therapy
  • SRT substrate reduction therapy
  • Gb3 like the other complex glycosphingolipids is synthesised from glucosylceramide (GlcCer) in the Golgi.
  • GlcCer glucosylceramide
  • FAPP2 a cytosolic transfer protein, has an important role in partitioning GlcCer into different pathways for downstream synthesis of different GSLs in different cellular compartments.
  • FAPP2 has been shown to be responsible for delivering GlcCer directly to the Trans Golgi network (TGN). In the TGN the globo- and asialo-sphingolipids, including Gb3, are synthesised from GlcCer.
  • GlcCer is moved through the vesicular route to the Golgi cisternae, to make the ganglio-series of sphingolipids in the Golgi cisternae. It has further been shown that FAPP-2 ⁇ / ⁇ mice have a selective decrease in Gb3 in the kidneys [7].
  • FAPP2 represents a target for SRT for the treatment of Fabry disease.
  • SRT has been proposed for lysosomal storage disorders such as Gaucher disease and Niemann-Pick type-C disease, and Zavesca® (Actelion) has been approved for the treatment of mild to moderate type-1 Gaucher disease patients who cannot receive the standard treatment of ERT and for the treatment of the neurological symptoms of the disease patients of all ages with Niemann-Pick type-C disease.
  • Inhibitors of FAPP2 that are suitable for SRT of Fabry disease are, however, not currently available.
  • a high resolution crystal structure of the GLTP domain of FAPP2 (FAPP2-C212) has now been generated.
  • the structure shows that the residues that interact with the sugar headgroup of GlcCer (including D360, N364, W407) are well refined and so are other (e.g. hydrophobic) residues that interact with the acyl/sphingosine chains of ceramide.
  • the high resolution structure can be used to design and to optimise inhibitors of FAPP2.
  • Atomic level structural information was not available for the GLTP domain of FAPP2 before the present invention and this information is crucial for understanding the structure-function relationships in FAPP2 activity and allows the design and testing of novel inhibitors of FAPP2.
  • the GLTP domain of FAPP2 is the C terminal 212 amino acids in human FAPP2 (residues 308-519 using the numbering of human FAPP2). It is particularly surprising that it has been possible to crystallise the GLTP domain of FAPP2, as this is a relatively flexible and unstable molecule (as evidenced by its low Tm) and it becomes completely unfolded even at around 45° C. Extensive previous efforts to generate crystals of the GLTP domain of FAPP2 were unsuccessful. Only when lysozyme T4L was chosen as a crystallisable fusion tag by the inventor was it possible to generate crystals, from which the structure as defined in more detail below was generated.
  • the invention provides a polypeptide comprising the GLTP domain of FAPP2, fused to T4L. Encoding nucleic acid molecules and vectors are further provided, as are host cells containing these.
  • a further aspect is the crystalline form of the polypeptide of the invention.
  • the invention provides a method of obtaining the crystalline form of the invention comprising providing a polypeptide of the invention, and concentrating the polypeptide to a polypeptide concentration at which it precipitates and forms crystals.
  • the crystalline form obtainable from this method is also provided.
  • the atomic coordinates provided herein for the GLTP domain of FAPP2, and subsets thereof and the three dimensional structural models that may be generated using the atomic coordinates provided herein can be used for identifying, designing, selecting, and/or optimising FAPP2 binding compounds. Such compounds could be used to inhibit FAPP2, and hence reduce Gb3 levels.
  • aspects of the invention thus relate to methods of identifying a compound that binds to FAPP2.
  • This method may comprise computationally identifying a compound that binds to FAPP2 using the atomic coordinates of at least the amino acids which make up the substrate binding pocket of FAPP2, e.g. as set forth in Table 2, or using the atomic coordinates for at least the GLTP domain of FAPP2, as set forth in Table 3.
  • a compound that binds to a FAPP2 polypeptide may be computationally identifying using said coordinates.
  • the invention provides a method of designing, selecting and/or optimising a compound that binds to FAPP2 comprising: a) providing a set of atomic coordinates of at least the amino acids which make up the substrate binding pocket of FAPP2, e.g. as set forth in Table 2 and b) computationally designing, selecting and/or optimising said compound by performing a fitting operation between said compound and all or part of the three dimensional structure information that is generated from the atomic coordinates.
  • the invention provides a method for evaluating the ability of a compound to associate with FAPP2 comprising: a) providing a set of atomic coordinates of at least the amino acids which make up the substrate binding pocket of FAPP2, e.g. as set forth in Table 2; b) computationally performing a fitting operation between said compound and all or part of the three dimensional structure information that is generated from the atomic coordinates; and c) analysing the results of said fitting operation to quantitate the association between the compound and FAPP2.
  • the invention provides a method for evaluating the ability of a compound to associate with FAPP2 comprising: a) providing a set of atomic coordinates for at least the GLTP domain of FAPP2 as set forth in Table 3 and b) computationally performing a fitting operation between said compound and all or part of the three dimensional structure information that is generated from the atomic coordinates; and c) analysing the results of said fitting operation to quantitate the association between the compound and FAPP2.
  • the invention provides a method of using a computer for evaluating the ability of a compound to associate with FAPP2 wherein said computer comprises a machine readable data storage medium comprising a data storage material encoded with the atomic coordinates of at least the amino acids which make up the substrate binding pocket of FAPP2, e.g.
  • means for generating a three dimensional graphical representation of the structure of said amino acids and said method comprises: a) positioning a first compound using a graphical three dimensional representation of the structure of the compound and all or part of the substrate binding pocket of FAPP2; b) performing a fitting operation between the compound and the substrate binding pocket of FAPP2 by employing computational means; and c) analysing the results of said fitting operation to quantitate the association between the compound and the substrate binding pocket of FAPP2.
  • the invention provides a method of using a computer for evaluating the ability of a compound to associate with FAPP2
  • said computer comprises a machine readable data storage medium comprising a data storage material encoded with the atomic coordinates for at least the GLTP domain of FAPP2 as set forth in Table 3 and means for generating a three dimensional graphical thereof and said method comprises: a) positioning a first compound using a graphical three dimensional representation of the structure of the compound and all or part of the GLTP domain of FAPP2; b) performing a fitting operation between said compound and the GLTP domain of FAPP2 by employing computational means; and c) analysing the results of said fitting operation to quantitate the association between said compound and the GLTP domain of FAPP2.
  • the invention provides a computer readable medium comprising the atomic coordinates for the polypeptide of the invention or a subset thereof, and a computer comprising the computer-readable medium of the invention.
  • a computer system comprising a memory unit comprising x-ray crystallographic structure coordinates defining the polypeptide of the invention or a subset thereof; and a processor in electrical communication with the memory unit; wherein the processor generates a molecular model having a three dimensional structure representative of at least a portion of said polypeptide also forms part of the invention.
  • a further aspect of the invention provides a method of producing a pharmaceutical composition comprising designing, selecting and/or optimising a compound with the methods of the invention, modifying the identified compound for administration as a pharmaceutical and formulating the product obtained with a pharmaceutically acceptable carrier or diluent.
  • the invention provides the use of the structure of the crystalline form of the invention or a portion of the structure in modelling a binding compound which binds to FAPP2, as well as the use of the atomic coordinates of the crystalline form of the invention or a subset of the atomic coordinates, in modelling a binding compound which binds to FAPP2.
  • a compound identified, designed, selected and/or optimised by a method of the invention, and optionally which has been modified for administration as a pharmaceutical, and/or which has been formulated as a pharmaceutical is provided in a further aspect of the invention.
  • Such compounds may be used as a medicament, e.g. in treating Fabry's disease.
  • Methods of treating or preventing Fabry's disease comprising administering an effective amount of such a compound or pharmaceutical to a patient in need thereof are furthermore provided.
  • T4L has advantages in that it allows crystals of this polypeptide to be generated for analysis.
  • T4L has previously been used as a fusion only with G protein coupled receptors (GPCR), either at the N-terminus or in the middle of the molecule [9,10,11]. These are proteins of a very different nature to the GLTP domain of FAPP2.
  • the invention thus provides a polypeptide comprising the GLTP domain of FAPP2, fused to a T4L polypeptide.
  • the GLTP domain of FAPP2 may be C terminal or N terminal to the T4L polypeptide.
  • the FAPP2 is human FAPP2.
  • the full length sequence for human FAPP2 is set out in SEQ ID NO:4.
  • the sequence of the C terminal 212 amino acids of human FAPP2 (amino acids 308-519 of FAPP2) which make up the GLTP domain is set out in SEQ ID NO:1 and the sequence of amino acids 2-164 of the T4L polypeptide is set out in SEQ ID NO:2.
  • the polypeptide has at least 95% sequence identity to the sequence SEQ ID NO:3.
  • the polypeptide of the invention comprises residues L349, D360 N364, K367, W407 R410, F414, I429, Y437, L441, H445, V449, F453, A456, F466, L470, V342, L346, V357, L361, L433, V452, L488, Y491, V345, N399, E403, R398, F311 and F312 in one embodiment, and in a further embodiment comprises sequence SEQ ID NO:3 or a fragment thereof.
  • the polypeptide of the invention consists of the sequence SEQ ID NO:3 or a fragment thereof.
  • the polypeptide consisting of the sequence SEQ ID NO:3 may be referred to as T4L-FAPP2-C212.
  • More preferred polypeptides have a percentage of identity of greater than 96%, 97%, 98%, 99% or 99.5%, respectively with the sequence of amino acids 308-519 of FAPP2 (SEQ ID NO:1) and/or amino acids 2-164 of lysozyme T4L (SEQ ID NO:2), and/or may have a percentage of identity of greater than 96%, 97%, 98%, 99% or 99.5%, respectively with the sequence of amino acids SEQ ID NO:3.
  • polypeptides may contain a sequence which differs from the reference sequences by amino acid substitutions, insertions or deletions from the reference sequence, for example, of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10, 15, 20 25, 30 or 35 or more amino acids, or up to this number of amino acids.
  • sequences include proteins containing conservative amino acid substitutions that do not affect the function or activity of the protein in an adverse manner.
  • Insertions may include linkers e.g. between the T4L sequence and the FAPP2 sequence.
  • Suitable examples of amino acids that may be used in linkers include threonine, serine, proline, asparagine, glycine.
  • the linker comprises one or more glycine residue. More preferably the linker consists of one or more glycine residue (e.g. is a single glycine).
  • Fragments of the reference polypeptides thus contain deletions (e.g. from the N or C terminus or internally) of up to 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids.
  • the polypeptide of the invention may additionally comprise a tag, e.g. of use in the preparation and/or purification of the peptide.
  • a tag e.g. of use in the preparation and/or purification of the peptide.
  • tags are well known in the art and thus include his tags.
  • a linker may also be present between any tag and the T4L sequence or FAPP2 sequence.
  • nucleic acids encoding the polypeptide of the invention are provided.
  • the nucleic acid comprises the sequence as set forth in SEQ ID NO: 5, or a fragment thereof.
  • substitutions, additions and deletions in the polypeptide of the invention may be generated by making appropriate changes to the encoding nucleic acid molecule of the invention and as such, the nucleic acid of the invention may comprise one or more nucleotide substitutions, additions, deletions, or duplications.
  • Modifications and mutations which create a polypeptide with a substitution, addition and/or deletions variant can be made within the nucleic acid sequence which encodes the polypeptide of the invention.
  • Modifications and mutations include deletions, point mutations, truncations, nucleic acid changes that lead to amino acid substitutions, and nucleic acid changes that lead to the addition of amino acids.
  • Nucleic acid modifications can be made to generate variants that are silent with respect to the amino acid sequence of the encoded polypeptide, but which provide preferred codons for translation in a particular host.
  • the preferred codons for translation of a nucleic acid in specific non-mammalian expression systems, such as prokaryotic systems, are well known in the art, e.g. [12;13;14].
  • Still other modifications can be made to the non-coding sequences to enhance or control the expression of the encoding gene.
  • the encoding nucleic acid sequence may be present in a vector.
  • the vector may include a coding sequence operably associated with one or more regulatory sequences.
  • a coding sequence and regulatory sequences are “operably associated with” when they are covalently linked to place the expression or transcription of the coding sequence under the control of the regulatory sequence.
  • a promoter region is operably associated with a coding sequence if the promoter region is capable of modulating transcription of the coding sequence.
  • 5′ non-transcribed regulatory sequences may include a promoter region which includes a promoter sequence for transcriptional control of the operably associated gene. Promoters may be constitutive or inducible. Regulatory sequences may also include enhancer sequences or upstream activator sequences.
  • a DNA sequence operably associated with a regulatory sequence may be inserted by restriction and ligation into a vector, e.g., for transport between different genetic environments or for expression in a host cell.
  • Vectors are typically composed of DNA or RNA.
  • Vectors include, but are not limited to, plasmids, viral vectors, cosmids, artificial chromosomes, and phagemids.
  • a cloning vector is one which is able to replicate in a host cell, and which is further characterized by one or more endonuclease restriction sites at which the vector may be cut and into which a desired nucleic acid sequence (e.g., an open reading frame) may be inserted.
  • Vectors may contain one or more marker sequences suitable for use in the identification of cells which have or have not been transformed or transfected with the vector.
  • Markers include, for example, genes encoding proteins which increase or decrease either resistance or sensitivity to antibiotics or other compounds, genes which encode enzymes whose activities are detectable by standard assays known in the art (e.g., ⁇ -galactosidase, alkaline phosphatase or luciferase), and genes which visibly affect the phenotype of transformed or transfected cells, hosts, colonies or plaques.
  • plasmid vectors that contain replication sites and control sequences derived from a species compatible with the host may be used.
  • the vector has the capacity to autonomously replicate in the host cell.
  • Useful prokaryotic hosts include bacteria such as E. coli .
  • To express a polypeptide in a prokaryotic cell it is desirable to operably join its nucleic acid sequence (e.g. cDNA) to a functional prokaryotic promoter.
  • a functional prokaryotic promoter may be either constitutive or regulatable (e.g. by induction or derepression).
  • Eukaryotic hosts include, for example, yeast, fungi, insect cells, and mammalian cells.
  • plant cells are also available as hosts, and control sequences compatible with plant cells are known in the art.
  • transcriptional and translational regulatory sequences may be employed, depending upon the nature of the host.
  • the transcriptional and translational regulatory signals may be derived from viral sources, such as adenovirus, bovine papilloma virus and simian virus. Mammalian promoters, such as, for example, actin, collagen, and myosin may be employed.
  • Transcriptional initiation regulatory signals may be selected which allow for repression or activation, so that expression of the gene sequences can be modulated, for example by regulatory signals, such as repression/initiation through changes in temperature or by addition of a chemical or biological modulating molecule.
  • Vectors can be employed which are capable of integrating a desired gene sequences into the host cell chromosome.
  • Cells which have stably integrated the introduced nucleic acid into their chromosomes can be selected by also introducing one or more markers which allow for selection of host cells which contain the expression vector.
  • the selectable marker gene sequence can either be directly linked to the gene sequences to be expressed, or introduced into the same cell by co-transfection. Additional elements, such as splice signals, transcription promoters, enhancers, and termination signals may also be needed for optimal synthesis of mRNA.
  • the vector or nucleic acid sequence is introduced into an appropriate host cell by any of a variety of suitable means, for example, transformation, transfection, conjugation, protoplast fusion, electroporation, calcium phosphate-precipitation, or direct microinjection.
  • recipient cells are grown in a selective medium, which selects for the growth of vector-containing cells. Expression of the cloned gene sequence results in the production of recombinant polypeptide.
  • the invention provides methods for crystallizing the polypeptide of the invention, e.g. by providing a polypeptide of the invention, and concentrating the polypeptide to a polypeptide concentration at which it precipitates and forms crystals.
  • methods for crystallizing the polypeptide of the invention involve crystallizing purified recombinant polypeptide of the invention.
  • crystallization conditions may be employed to provide crystals of the polypeptide of the invention, therefore, a wide variety of crystallization conditions are envisioned and encompassed by the present invention. Every protein crystallizes under a unique set of conditions, such as, for example, supersaturating the solution containing the protein; and/or adding precipitating or crystallizing agents, salts, metals, and/or buffers to the solution containing the protein.
  • any crystallization technique known to those skilled in the art may be employed to obtain the crystals of the present invention, including, but not limited to, batch crystallization, vapor diffusion (e.g., either by sitting drop or hanging drop), and micro dialysis. Seeding in some instances may be required to obtain x-ray quality crystals. Standard micro and/or macro seeding of crystals may therefore be used.
  • the crystals of the present invention are grown using the hanging-drop vapor-diffusion method.
  • the crystals of the polypeptide of the invention may be grown at any temperature suitable for crystallization.
  • the crystals may be grown at temperatures ranging from approximately 0° C. to approximately 30° C.
  • the crystals of the present invention are grown at a temperature of between approximately 0° C. to approximately 10° C.
  • the crystals of the present invention are grown at a temperature of between approximately 0° C. to approximately 5° C.
  • the crystals of the present invention are grown at a temperature of between approximately 5° C.-approximately 10° C., approximately 10° C. to approximately 15° C., approximately 15° C. to approximately 20° C., approximately 20° C. to approximately 25° C., approximately 25° C. to approximately 30° C.
  • the crystals of the present invention are grown at a temperature of approximately, 10° C., 11° C., 12° C., 13° C., 14° C., 15° C., 16° C., 17° C., 18° C., 19° C., 20° C. or room temperature.
  • Crystals of the present invention are typically grown from a crystallization solution comprising one or more precipitants.
  • the precipitants may be selected from polymers, polyethers, alcohols, salts, and/or polyols.
  • these precipitants are selected from the group consisting of monomethyl ether (ME); polyethylene glycol PEG-400; PEG-1000; PEG-2000; PEG-3000; PEG-8000; PEG 20,000; ((NH 4 ) 2 SO 4 ); 2-propanol; 1,4-butanediol; K/Na tartrate; ethanol; NaCl; sodium citrate; NaH 2 PO 4 /K 2 HPO 4 ; ethylene glycol; dioxane; 2-methyl-2,4-pentanediol (MPD); polyethyleneimine; tert-butanol; and 1,6-hexanediol.
  • MPD monomethyl ether
  • the crystallization conditions may further comprise one or more salts.
  • the crystallization conditions further comprises one or more salts selected from the group consisting of MgCl 2 ; Zn(OAc) 2 , Li SO 4 , Ca(OAc) 2 , NaCl; (NH 4 ) 2 SO 4 , CdCl 2 , CoCl 2 , MgSO 4 , and NiCl 2 , preferably MgCl 2 and/or NaCl.
  • the crystallization conditions further comprises one or more buffers selected from the group consisting of 2-(cyclohexylamino)ethanesulfonic acid (CHES); 2-(N-morpholino)ethanesulfonic acid (MES); N-cyclohexyl-3-aminopropanesulfonic acid (CAPS); N-cyclohexyl-2-hydroxyl3-aminopropanesulfonic acid (CASPO); 4-(2-hydroxyethyl)piperazine-1-ethane sulfonic acid (HEPES); 3-(N-morpholino)propanesulfonic acid (MOPS); 2-amino-2-(hydroxymethyl)-1,3-propanediol (Tris); piperazine-N,N′-bis(2-ethanesulfonic acid) (PIPES); N-(2-Acetamido)-2-aminoethanesulfonic acid (ACES); N,N-Bis(2-hydroxyethyl) buffers
  • Precipitants that may be used to crystallize the polypeptide of the invention include, but are not limited to, lithium sulfate; PEG-400; PEG-550 MME; PEG-2000; PEG-6000; PEG-8000; PEG 20,000; and/or 2-methyl-2,4-pentanediol (MPD).
  • MPD 2-methyl-2,4-pentanediol
  • the pH of the crystallization solution is between about a pH of approximately 4 to pH of approximately 9. In certain embodiments, the pH of the crystallization solution is between about a pH of approximately 6.5 to a pH of approximately 9. In certain embodiments, the pH of the crystallization solution is approximately 7.0. In certain embodiments, the pH of the crystallization solution is near the isoelectric point of the protein.
  • the polypeptide of the invention at a concentration of about 6 mg/ml is screened for crystallization conditions using the sitting drop vapor diffusion method employing a random matrix crystallization screening kit.
  • a random matrix crystallization screening kit Such kits are commercially available, for example, Qiagen JCSG-I random matrix crystallisation kit.
  • the polypeptide of the invention is crystallized under #6 conditions (0.2 M MgCl 2 , 0.1 M Tris, pH 7.0, 2.5M NaCl). In other embodiments the conditions are 0.1-0.3M MgCl 2 , 1.5-3M NaCl, 0.1M Tris pH7. Approximately 6-20 mg/ml protein may be used
  • the crystals are screened for optimal cryo-conditions to freeze the crystals at the temperature of liquid nitrogen, for example, to attenuate the radiation damage to crystals that occurs during data collection.
  • screening for optimal cryo-conditions can be carried out in crystallization buffers containing 20-35% v/v of polyols, such as glycerol, ethylene glycol or 2-methyl-2,4-pentanediol (MPD), or 35-70% w/v of sugars, such as sucrose or xylitol. Crystals may be soaked in the cryo-buffer for about 5-15 minutes.
  • cryo-protection of crystals of the invention, grown in condition #6 (0.2 M MgCl 2 , 0.1 M Tris, pH 7.0, 2.5M NaCl) is achieved by soaking the crystals in a cryo-buffer containing glycerol and xylitol (0.2 M MgCl 2 , 0.1 M Tris, pH 7.0, 2.5M NaCl, 10% glycerol and 5% xylitol).
  • the crystals of the invention may also include a binding compound bound to the GLTP domain of FAPP2 polypeptide.
  • the complex of the polypeptide and binding compound may be formed before, after, or during crystallization.
  • the crystals of the present invention and the crystallization conditions further comprise a binding compound.
  • the crystallization solution of the above method further comprises a binding compound in order to provide a FAPP2 GLTP domain polypeptide-binding compound complex.
  • the FAPP2 GLTP domain polypeptide provided by the above method is soaked in a solution of a binding compound to provide a FAPP2 GLTP domain polypeptide-binding compound complex.
  • a binding compound is bound in the substrate binding pocket of FAPP2 GLTP domain polypeptide.
  • the inhibitor is a reversible inhibitor.
  • the binding compound is bound outside the substrate binding pocket at one or more exosites. In some embodiments, the binding compound, whether bound in the substrate binding pocket or at one or more exo sites, aids in stabilizing the protein for crystallization and/or x-ray diffraction.
  • the step of providing the polypeptide of the invention may optionally comprise expressing an appropriate polypeptide in a host cell and may optionally further comprise purifying said polypeptide.
  • the polypeptide which is expressed is any polypeptide from which the polypeptide of the invention may then be derived, e.g. by proteolytic cleavage.
  • the polypeptide which is expressed may thus contain a tag, which is subsequently removed during or following purification of the protein from the host cell.
  • the tag may be used to facilitate purification e.g. by allowing binding to a matrix, or by allowing secretion of the polypeptide from the host cell.
  • Ni column step Ni column binds to histidine resides, e.g. in a his tag.
  • a size exclusion chromatography step (SEC) step may also be used, e.g. to separate polypeptides of different sizes.
  • An anion exchange column may additionally or alternatively be used e.g. after the Ni-column. This may increase the purity of the protein.
  • the invention also provides a crystalline form of the polypeptide of the invention.
  • the crystals are of the GLTP domain of human FAPP2, fused to a T4L polypeptide.
  • the crystals are of a polypeptide comprising or consisting of the amino acid sequence set forth in SEQ ID NO: 3.
  • a crystal of the present invention may take a variety of forms, all of which are contemplated by the present invention.
  • the crystal may have a size of about 50-100 ⁇ 30-50 ⁇ 20-30 ⁇ m.
  • the crystals have the optical appearance as illustrated in FIG. 5 and/or the crystals may grow as rod shaped, some without clear faces.
  • a crystal of the present invention may be obtainable by the methods of polypeptide crystallization referred to elsewhere herein.
  • space group refers to the arrangement of symmetry elements in a crystal.
  • unit cell refers to the basic parallelipiped shaped block. The entire volume of a crystal may be constructed by regular assembly of such blocks.
  • the present invention provides three-dimensional structural information for the polypeptide of the invention.
  • the invention provides three-dimensional structural information for a subset of amino acids of the polypeptide of the invention.
  • this subset may be the amino acids making up the substrate binding pocket of FAPP2, the amino acids making up the sugar headgroup recognition site of FAPP2, and/or the amino acids making up the GLTP domain of FAPP2.
  • X-ray diffraction data collection can be performed in an X-ray crystallography facility.
  • One, two, three, or more diffraction data sets may be collected from one or more crystals.
  • the crystals of the present invention diffract to a resolution limit of at least approximately 8 angstrom ( ⁇ ). In certain embodiments, the crystals diffract to a resolution limit of at least approximately 6 ⁇ , 4 ⁇ or 3 ⁇ .
  • the crystal diffracts x-rays for a determination of structural coordinates to a maximum resolution of about 3.9 ⁇ , of about 3.2 ⁇ , of about 2.9 ⁇ , or about 2.6 ⁇ .
  • the crystals may diffract to a maximum resolution of about 2.0-4.0 ⁇ (e.g. about 2.5 ⁇ to about 3.5 ⁇ , of about 2.0 ⁇ to about 3.0 ⁇ , of about 2.5 ⁇ to about 3.0 ⁇ , or of about 3.0 ⁇ to about 3.5 ⁇ ).
  • Diffraction data can be collected using a variable oscillation angles, number of frames and exposure times that all depend on the equipment used and on the quality of the crystal(s) used to collect the data. One of ordinary skill would know how to optimize these parameters [16; 17]).
  • diffraction data can be collected with 1° oscillation. Other oscillation may be used, e.g. oscillations of less than or greater than 1°.
  • diffraction data can be collected with 0.1°, 0.3°, 0.5°, 1°, 1.5°, 2°, 3°, 4°, 5°, or 10° oscillation, or any oscillation angle in between these angles.
  • 120 frames are collected. More or fewer than 120 frames may be collected.
  • 10, 20, 50, 100, 200, 300. 400, 500, 1000, or 5000 frames may be collected, or any number of frames in between these numbers.
  • the exposure is 10 minutes per frame.
  • Other frame exposure times may also be used, such as, for example 5 seconds, 10 seconds, 20 seconds, 30 seconds, 40 seconds, 50 seconds, 60 seconds, 120 seconds, 180 seconds, 3 minutes, 4 minutes, 5 minutes, 15 minutes, 20 minutes, 30 minutes per frame or any exposure time in between these times.
  • Data merging and scaling can be done, for example, using HKL2000 software suite (HKL Research, Inc., Charlottesville, Va.).
  • Structure determination, model building, and refinement can be performed, for example, using software such as Molrep, coot and Refmac that are part of CCP4 software suite.
  • MolRep is a program for automated molecular replacement (e.g., MolRep, version 10.2.35).
  • Coot Graphical Interface by Paul Emsley www.ysbl.york.ac.uk/ ⁇ emsley
  • model building includes an interface to refmac5 (Gnu Public License; refmac5, e.g. version 5.5.0072 or version 5.5.0109).
  • a macromolecular refinement program by Garib Murshudov et al. is integrated into the CCP4 program suite (www.ccp4.ac.uk, CCP4, version 6.1.3).
  • models of the polypeptide may be obtained by the molecular replacement method using the program Molrep and the structural information available for T4L (PDB ID:3G3V) and human GLTP (PDB ID 1SWX) as search models.
  • initial phases may be obtained removing from the coordinates of the search models all of the side chains resulting in a poly-alanine model.
  • Such models may be used for further model building and refinement, for example using programs such as coot and Refmac.
  • molecular replacement refers to a method that involves generating a preliminary model of the three-dimensional structure of a polypeptide or a polypeptide complexed with a binding compound whose structure coordinates are not known by orienting and positioning a polypeptide structure whose atomic coordinates are known. Phases are calculated from this model and combined with the observed amplitudes of the unknown crystal structure to give an approximate structure. This structure is then subject to any of several forms of refinement to provide a final, accurate structure. Any program known to the skilled artisan may be employed to determine the structure by molecular replacement. Suitable molecular replacement programs include, but are not limited to, AMORE (1994) [18;19] and CNS (1998) [20].
  • the atomic coordinates of the crystalline polypeptide of the invention, or a subset thereof are provided.
  • the crystal diffracts at a resolution of 3 ⁇ the model may be refined to a final R factor of 25.5% and Rfree of 32.4%.
  • the crystal diffracts at a resolution of 2.6 ⁇ the model may be refined to a final R factor of 20.5% and Rfree of 25.7%.
  • atomic coordinates of crystalline T4L-FAPP2-C212 are provided.
  • the parameters for residues 36-207 of SEQ ID NO:3 are set forth in Table 1, in which they are referred to as residues 136-307 to reflect their positions relative to residues 308 onwards of human FAPP2 in the fusion protein.
  • the parameters for substrate binding pocket residues are set forth in Table 2 and the parameters for the GLTP domain of FAPP2 are set forth in Table 3.
  • Residue numbering in Tables 2 and 3 is accordance with residue numbering in full length human FAPP2 (residues 308 onwards are referred to with numbering that is used for these residues in full length human FAPP2 (e.g. 308 is Ile, 309 is Pro, 310 is Thr, 311 and 312 are both Phe etc.).
  • Atomic coordinates for residues 308-514 of human FAPP2 are provided in Table 3. Only the coordinates for the molecule A are provided.
  • atomic coordinates refers to mathematical coordinates derived from mathematical equations related to the patterns obtained on diffraction of a monochromatic beam of X-rays by the atoms (scattering centers) of a protein molecule in crystal form.
  • the diffraction data are used to calculate an electron density map of the repeating unit of the crystal.
  • the electron density map is then used to establish the positions of the individual atoms within the unit cell of the crystal.
  • the coordinates can also be obtained by means of computational analysis.
  • Crystalline T4L-FAPP2-C212 has two molecules of T4L-FAPP2-C212 in the asymmetric unit, referred as Mol-A and Mol-B ( FIG. 1 ). T4L from adjacent molecules in the crystal lattice make extensive contacts that appear to have facilitated crystallization ( FIG. 1 ). Only the coordinates for the molecule A are shown in the Tables.
  • the FAPP2-C212 structure takes the general GLTP fold with eight alpha helices ( FIG. 6 ).
  • W407 is located in helix-4.
  • the sugar head group would stack on this tryptophan and further makes contacts with D360 and N364.
  • E403 is also located at the sugar binding pocket which would provide additional interaction with the sugar ring.
  • E403 has been reported in the literature, based on homology modeling, as being located in the sugar binding pocket and as being able to discriminate negatively charged sugar head groups. However in the present structure, it appears as a residue that could stabilise sugar ring binding.
  • K367 that is hydrogen bonded with N399 and the projected loop around N399 appear to be responsible for discriminating negatively charged sugar head groups in FAPP2 ( FIG. 7 ).
  • F311 of FAPP2 takes the same place as F33 of hGLTP located in between helices 1 and 2. These two residues may play a role in ceramide release. Inhibition of the transfer activity of FAPP2 may be achieved by displacing them.
  • binding pocket is used herein to refer to the site at which the molecule to be transferred (i.e. the substrate) binds to FAPP2.
  • the structure and chemical properties of the binding pocket allow the recognition and binding of a binding compound or substrate.
  • the binding pocket typically includes residues responsible for the binding specificity (e.g., charge, hydrophobicity, and/or steric hindrance) of the molecule. 30 residues have been identified by the inventor as being within 5 ⁇ of the docked substrate in the ceramide docked model (see Table 4).
  • the substrate binding pocket comprises the residues of Table 4. These residues have the potential to make contact with the substrate.
  • the binding pocket may be defined as comprising the sugar headgroup binding residues.
  • the sugar headgroup binding residues are residues which make contact with the glucosyl headgroup of the substrate (e.g. GlcCer). At least residues D360, N364, and W407 are believed to make contact with the glucosyl head group of GlcCer, based on mutational studies on hGLTP [21] (see also FIG. 3 ).
  • the sugar headgroup binding residues may contribute to selectivity of FAPP2 for certain substrates. For example it has been shown that FAPP2 shows a different substrate selectivity to the related molecule GLTP. FAPP2 shows a preference for uncharged monohexosyl and dihexosylceramides, compared to the broadly selective human GLTP [8].
  • FAPP2 has been shown to efficiently transfer GlcCer and other simple neutral glycosylceramides such as GlaCer and LacCer, but not negatively charged molecules such as sulfatide.
  • the atomic coordinates of the sugar headgroup binding residues are included in Table 2.
  • the substrate binding pocket may also comprise residues that allow FAPP2 to accommodate the non-sugar portion of the substrate such as GlcCer, e.g. the ceramide portion thereof.
  • a substrate or ceramide (fatty acid chain) accommodating tunnel is present, which comprises hydrophobic residues (see Table 4). This tunnel, which may be defined as being hydrophobic, will have a shape which depends on substrate binding (helices 2, 4, 5 and 6 can slightly move to accommodate fatty acid chains). The role of the two key phenylalanine resides F311 and F312 in the ceramide accommodating tunnel is discussed above. Residues in the ceramide accommodating tunnel include L441, F453, Y491 (as identified e.g. in [21]), in addition to other hydrophobic residues referred to in Table 4).
  • the present structure has identified V345, N399, E403, R398, F311 and F312 as residues of the substrate binding pocket which are unique to human FAPP2 compared to human GLTP. They may be absent from human GLTP (in the case of R398, F311 and F312) or different to the equivalent residues in human GLTP. The potential role of F311 and F312 is discussed above. N399, E403 and R398 are found near to the sugar headgroup.
  • the model created based on the structural information obtained contains positional information for the sugar headgroup binding residues. In other embodiments the model created based on the structural information obtained additionally or alternatively contains positional information for residues in the ceramide accommodating tunnel, including L441, F453, Y491 (and optionally other hydrophobic residues referred to in Table 4). In further embodiments the model created based on the structural information obtained additionally or alternatively contains positional information of the residues referred to in Table 4 as unique to human FAPP2.
  • Tables 1-3 provide atomic coordinates for crystalline T4L-FAPP2-C212 and portions thereof, the present invention also contemplates structural modifications thereof, for example, for polypeptides having significant structural homology (e.g., significant structural overlap), particularly in the areas recognized as active, and thus providing the same or similar structural information as provided herewith.
  • Significant structural homology refers to at least one of the following criteria: (i) at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% structural homology with crystalline T4L-FAPP2-C212 or the GLTP domain thereof; or (ii) at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% structural homology with a recognized binding pocket of crystalline T4L-FAPP2-C212 or the GLTP domain thereof.
  • significant structural homology may also refer to at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% structural homology with the primary amino acid sequence of T4L-FAPP2-C212 or the GLTP domain thereof.
  • the primary amino acid sequence of T4L-FAPP2-C212 may be a sequence included as a segment in a larger amino acid sequence, or may be a fragment thereof (e.g. the GLTP domain).
  • a fragment of a full-length, T4L-FAPP2-C212 polypeptide is provided or used in an inventive method or system provided herein.
  • a fragment comprises a sequence of (or of at least) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 50-75, 75-100, 100-150, 150-200 amino acids.
  • a fragment of T4L-FAPP2-C212 does not comprise a full-length T4L-FAPP2-C212 sequence, for example, a full-length human T4L-FAPP2-C212 sequence.
  • a fragment of T4L-FAPP2-C212 comprises all or at least part of the portion responsible for the transfer activity of FAPP2.
  • fragments include fragments that contain the residues that have been shown to make contact with the glucosyl head group of GlcCer (e.g. D360, N364, W407)
  • the present invention contemplates any and all such variations and modifications of T4L-FAPP2-C212 or the GLTP domain thereof, and which may be used in the methods and uses of the invention (e.g. 308-515, 308-514, 308-513, 308-512 of FAPP2).
  • Table 1 provides a set of atomic coordinates for T4L-FAPP2-C212 and Table 3 provides the atomic coordinates for the GLTP domain thereof.
  • the invention provides methods and/or uses of the structural information, for example methods for designing, identifying, and/or screening binding compounds to FAPP2 that may be useful in treating Fabry disease.
  • binding compounds may be useful in the treatment of Fabry disease. Since Fabry disease is caused by the absence of ⁇ -galactosidase A ( ⁇ -Gal A), an enzyme required for the normal processing of glycosphingolipids in mammalian lysosomes, reducing the amount of substrate for this enzyme may be particularly useful in the treatment of Fabry disease.
  • the binding compound may affect enzyme stabilization, e.g. during protein folding. The compound may also affect aspects of intracellular trafficking of the enzyme or aspects of transfer function, such as substrate recognition and/or transfer activity.
  • methods are provided for the in silico design, identification, selection and/or optimisation of FAPP2 binding compounds using the three-dimensional structural information provided herein.
  • methods are provided that can be used to identify inhibitors, reversible inhibitors, activators and/or stabilizers of FAPP2 activity.
  • methods are provided that can be used to identify binding compounds that modulate FAPP2 stability.
  • methods are provided that can be used to identify binding compounds that modulate FAPP2 stability, activity, and/or intracellular trafficking.
  • methods are provided that can be used to test potential binding compounds for their ability to bind to, to modulate stability, to modulate activity, and or to modulate intracellular trafficking of FAPP2.
  • these methods include in silico, in vitro, and in vivo methods.
  • FAPP2 is referred to herein it is preferably human FAPP2.
  • Compounds obtained from this method may further be identified as being able to treat Fabry disease in human subjects.
  • the methods may utilise the atomic coordinates of at least the amino acids which are the sugar headgroup binding residues and/or additional residues in the substrate binding pocket.
  • Table 3 provides the atomic coordinates for residues 308-514 of human FAPP2. The methods may utilise these atomic coordinates of at least amino acids 308-514 of human FAPP2.
  • the invention thus provides a method of identifying a compound that binds to FAPP2, comprising computationally identifying a compound that binds to FAPP2 using the atomic coordinates of at least the substrate binding pocket of FAPP2, e.g. as set forth in Table 2.
  • the invention further provides a method of identifying a compound that binds to FAPP2, comprising a) providing a set of atomic coordinates for at least the GLTP domain of FAPP2, as set forth in Table 3 and b) computationally identifying a compound that binds to FAPP2 using said coordinates.
  • the invention provides a method of designing, selecting and/or optimising a compound that binds to FAPP2 comprising: a) providing a set of atomic coordinates of at least the amino acids which make up the substrate binding pocket of FAPP2, e.g. as set forth in Table 2 and b) computationally designing, selecting and/or optimising said compound by performing a fitting operation between said compound and all of part of the three dimensional structure information that is generated from the atomic coordinates.
  • the invention further provides a method of designing, selecting and/or optimising a compound that binds to FAPP2 comprising: a) providing a set of atomic coordinates for at least the GLTP domain of FAPP2 as set forth in Table 3 and b) computationally designing, selecting and/or optimising said compound by performing a fitting operation between said compound and all or part of the three dimensional structure information that is generated from the atomic coordinates.
  • the invention provides a method for evaluating the ability of a compound to associate with FAPP2 comprising: a) providing a set of atomic coordinates of at least the amino acids which make up the substrate binding pocket of FAPP2, e.g. as set forth in Table 2; b) computationally performing a fitting operation between said compound and all or part of the three dimensional structure information that is generated from the atomic coordinates; and c) analysing the results of said fitting operation to quantitate the association between the compound and said FAPP2 polypeptide.
  • the invention further provides a method for evaluating the ability of a compound to associate with FAPP2 comprising: a) providing a set of atomic coordinates for at least the GLTP domain of FAPP2 as set forth in Table 3 and b) computationally performing a fitting operation between said compound and all or part of the three dimensional structure information that is generated from the atomic coordinates; and c) analysing the results of said fitting operation to quantitate the association between the compound and FAPP2.
  • the methods of the invention further comprise generating a three dimensional graphical representation of the structure prior to step (b).
  • the invention provides a method of using a computer for evaluating the ability of a compound to associate with FAPP2 wherein said computer comprises a machine readable data storage medium comprising a data storage material encoded with the atomic coordinates of at least the amino acids which make up substrate binding pocket of FAPP2, e.g.
  • means for generating a three dimensional graphical representation of the structure of said amino acids and said method comprises: a) positioning a first compound using a graphical three dimensional representation of the structure of the compound and all or part of the substrate binding pocket of FAPP2; b) performing a fitting operation between the compound and the substrate binding pocket of FAPP2 by employing computational means; and c) analysing the results of said fitting operation to quantitate the association between the compound and the substrate binding pocket of FAPP2.
  • the method further provides a method of using a computer for evaluating the ability of a compound to associate with FAPP2
  • said computer comprises a machine readable data storage medium comprising a data storage material encoded with the atomic coordinates for at least the GLTP domain of FAPP2 as set forth in Table 3 and means for generating a three dimensional graphical representation of the structure of the GLTP domain of FAPP2 and said method comprises: a) positioning a first compound using a graphical three dimensional representation of the structure of the compound and all or part of the GLTP domain of FAPP2; b) performing a fitting operation between said compound and the GLTP domain of FAPP2 by employing computational means; and c) analysing the results of said fitting operation to quantitate the association between said compound and the GLTP domain of FAPP2.
  • the method of using a computer for evaluating the ability of a compound to associate with FAPP2 may further comprise the steps of (d) repeating steps (a) to (c) with a second chemical entity; and (e) selecting at least one of the first or second chemical entity that associates with the GLTP domain of FAPP2 or the substrate binding pocket based on the quantitated association of the first or second chemical entity.
  • the above methods may additionally be performed based on the atomic coordinates of the sugar head group binding residues alone, or with the ceramide accommodating tunnel residues and/or the residues defined as unique to FAPP2.
  • Useful subsets of structure coordinates that can be used in the method of the invention include structure coordinates defining a) are the sugar headgroup binding residues of FAPP2 b) the substrate binding pocket residues of FAPP2 and c) the GLTP domain of FAPP2.
  • a potential binding compound according to this invention may bind anywhere on FAPP2.
  • a potential binding compound according to this invention may bind on the GLTP domain of FAPP2.
  • the binding compound may bind to the binding pocket or to any other site which is not identified as a binding pocket, e.g. to a site which is adjacent to a binding pocket.
  • the potential binding compound according to this invention may bind specifically to one or more sites on the FAPP2 polypeptide (be it nascent, partially or fully folded).
  • the binding molecule will bind to the binding pocket of FAPP2. In many embodiments the binding molecule will bind to the sugar headgroup binding residues, of FAPP2, or the ceramide accommodating tunnel residues. “Binding to” a molecule or a defined portion thereof encompasses binding to all or a part of a molecule or a defined portion thereof, such that reference to binding to a molecule or a defined portion thereof does not require an interaction to be made with each residue of that molecule or portion.
  • binding compounds may use information about the relevant molecule or the defined portion thereof, or a part of the defined molecule or portion thereof. It may thus use information about the structure of the GLTP domain of FAPP2, the structure of the binding pocket of FAPP2, the structure of the sugar headgroup binding residues, or a portion of any of these.
  • a “binding compound” refers to a compound which reversibly or irreversibly binds to FAPP2. In certain embodiments, the binding compound binds in a binding pocket of FAPP2. Binding may involve the formation of bonds which may be covalent or non-covalent. Non-covalent bonds may be e.g. hydrogen bonds, ionic binds or hydrophobic bonds.
  • a binding compound may affect the activity of FAPP2. This may be achieved directly by modulating the ability of the FAPP2 to transfer its substrate, which may be achieved by being an inhibitor of FAPP2 (i.e. eliciting inhibition or reduction in transfer activity), or an activator of FAPP2 (i.e. eliciting an increase in transfer activity).
  • the binding compound may affect the stability of FAPP2 which in turn may result in an effect on the activity of FAPP2 in which case the binding molecule is a stabilizer or destabilizer of FAPP2 (i.e. may elicit a change in stability of FAPP2).
  • the binding molecule may affect the intracellular trafficking of FAPP2.
  • FAPP2 picks up its substrate in the Golgi, so binding molecules which influence the ability of FAPP2 to localise at the Golgi (e.g. which prevent FAPP2 from localizing to the Golgi, or which reduce the ability of FAPP2 to localise to the Golgi, or which increase the ability of FAPP2 to localise to the Golgi) are also contemplated.
  • the potential binding compound is a potential inhibitor or activator compound. In certain embodiments, the potential binding compound is a potential FAPP2 inhibitor or activator compound. In certain embodiments, the potential inhibitor or activator compound is a competitive, uncompetitive or non-competitive inhibitor or activator compound. In certain embodiments, the potential inhibitor is a reversible inhibitor. Those of skill in the art may identify potential inhibitors or activators as competitive, uncompetitive or non-competitive or reversible inhibitors or activators by computer fitting kinetic data using standard equations [22], or by employing assays which measure the ability of a potential inhibitor or activator to modulate FAPP2 transfer activity.
  • FAPP2 is known to at least function to transfer glycolipids such as GlcCer from the cis-Golgi to the TGN.
  • the activity of FAPP2 thus includes its transfer activity, i.e. transferring its substrate from one membrane to another membrane. This transfer activity can be measured by measuring the substrate transfer in vitro, e.g. from one membrane to another.
  • the assays in general involve donor and acceptor vesicles and the transfer of labelled substrate is measured. At least two established assays exist. In one example substrate transfer is measured by liquid scintillation counting of acceptor vesicles when the substrate is radiolabeled.
  • FRET Förster resonance energy transfer
  • Inhibitors or activators of FAPP2 may in one embodiment lead to a statistically significant decrease or increase, respectively of FAPP2 activity.
  • An inhibitor of FAPP2 may be a catalytic substrate of FAPP2.
  • Such compounds may be analogues of the natural substrate of FAPP2, GlcCer, or of other molecules which bind to the binding pocket e.g. GalCer or LacCer.
  • Such analogues may have modifications which cause them to inhibit FAPP2.
  • inhibitors include molecules with a hydrophilic or hydrogen bond forming head group, e.g. that can stack over W407 and fill the sugar headgroup binding pocket; (2) hydrophobic molecules that can bind to the ceramide accommodating tunnel; (3) small molecules that can displace F311/F312 located at the end of ceramide accommodating tunnel (at the opposite face to sugar binding pocket).
  • a binding compound may be a small molecule.
  • small molecule as used herein is meant to describe a low molecular weight organic compound which is not a polymer.
  • a small molecule may bind with high or low affinity to a biopolymer such as protein, nucleic acid, or polysaccharide and may in addition alter the activity or function of the biopolymer.
  • the molecular weight of the small organic compound may generally be smaller than about 1500 Da. Small molecules may be smaller than about 1000 Da, smaller than about 800 Da, or smaller than about 500 Da. Small molecules may rapidly diffuse across cell membranes and may have oral bioavailability. These compounds can be natural or synthetic.
  • binding molecules that are specific to FAPP2 (e.g. to human FAPP2).
  • FAPP2 e.g. to human FAPP2
  • binding molecule has a preference for binding to FAPP2 (e.g. it does not bind to one or more other molecules or it shows reduced binding e.g. at least 5, 10, 20, 50, 100, 200, 500, 1000 fold reduced affinity to the one or more other molecules). Binding can be quantitated in accordance with methods known in the art.
  • the binding molecule is specific for FAPP2 in comparison to GLTP (e.g. specific for human FAPP2 in comparison to human GLTP).
  • the GLTP domain of human FAPP2 is similar in structure to human GLTP, but not identical, as determined by the inventor, and there are key differences between these two molecules.
  • the identification of the structure of FAPP2 by the inventor means that binding molecules that have a required specificity can be obtained.
  • the availability of structural information for human GLTP also means that in addition to the methods above (using the structure of the GLTP domain of human FAPP2 (or portions thereof)) methods can be carried out in which the steps described above using the atomic coordinates or structural information for the GLTP domain of human FAPP2 (or portions thereof) are carried out using the atomic coordinates or structural information for human GLTP. This can be done in parallel or in sequence with methods using the structure of the GLTP domain of human FAPP2 (or portions thereof). Such methods are a further way to determine whether a binding molecule that binds to FAPP2 is specific for FAPP2 over GLTP.
  • the information provided herein can be used to identify binding compounds which bind to both human GLTP and human FAPP2 (e.g. with equal or about equal affinity), or which are specific for human GLTP over human FAPP2.
  • the methods referred to above can be carried out using the atomic coordinates or structural information available for GLTP, and the equivalent information provided herein for FAPP2, simultaneously or sequentially, to identify binding compounds which bind to both human GLTP and human FAPP2, or which are specific for human GLTP over human FAPP2.
  • methods referred to above which identify, design, select, optimise and/or evaluate a compound that binds to FAPP2 may thus additionally comprise a step of determining whether said compound binds to GLTP, and/or performing a fitting operation between the compound and all or part of the three dimensional structural information of GLTP.
  • Methods referred to above which relate to using a computer for evaluating the ability of a compound to associate with FAPP2 may additionally require the data storage material to be encoded with the atomic coordinates of at least the amino acids which make up the substrate binding pocket of GLTP (or the whole molecule) and additionally require the steps to quantitate the association between the compound and the substrate binding pocket of GLTP.
  • Uses referred to above may additionally incorporate the use of the structure of GLTP.
  • Such methods and uses may thus be methods which identify, design, select, optimise and/or evaluate a compound that binds specifically to FAPP2 (e.g. over GLTP), or which binds to FAPP2 and GLTP.
  • a method of identifying a compound that binds specifically to GLTP over FAPP2 comprises computationally identifying a compound that binds specifically to GLTP over FAPP2 using (i) the atomic coordinates of at least the substrate binding pocket of FAPP2, e.g. as set forth in Table 2 and the atomic coordinates of at least the substrate binding pocket of GLTP or (ii) the atomic coordinates for at least the GLTP domain of FAPP2, as set forth in Table 3 and the atomic coordinates for GLTP.
  • a method of designing, selecting and/or optimising a compound that binds specifically to GLTP over FAPP2 may comprise: a) providing a set of atomic coordinates of i) at least the amino acids which make up the substrate binding pocket of FAPP2, e.g. as set forth in Table 2 and at least the amino acids which make up the substrate binding pocket of GLTP, or ii) at least the GLTP domain of FAPP2 as set forth in Table 3, and GLTP b) computationally designing, selecting and/or optimising said compound by performing a fitting operation between said compound and all of part of the three dimensional structure information that is generated from the atomic coordinates.
  • the methods of the invention further comprise generating a three dimensional graphical representation of the structure prior to step (b).
  • the potential binding compound may be identified or selected from a library of compounds, or identified or selected from a database. In such cases the identification is made from a pre-existing molecular structure and the potential binding compound is chosen, for example, from a group of pre-existing compounds. One or more members, such as a small molecule or a substrate analogue that have or exhibit a desired property or characteristic are chosen.
  • the potential binding compound is in some embodiments designed, e.g. in silico. When the binding compound is designed in silico this may be from a known compound. “Design” or “designing” as used herein is meant to provide a novel molecular structure of, for example, a compound, such as a small molecule or a substrate analogue.
  • Suitable computer programs which may be used in the design and identification of potential binding compounds include, but are not limited to, GRID [28], MCSS [29], AUTODOCK [30]; and DOCK [31].
  • Suitable computer programs which may be used in connecting the individual chemical entities or fragments include, but are not limited to, CAVEAT (Bartlett, (1989) Molecular Recognition in Chemical and Biological Problems, Special Pub., Royal Chem. Soc. 78:182-19632); and 3D Database systems such as MACCS-3D by MDL Information Systems, San Leandro, Calif.), HOOK (Molecular Simulations, Burlington, Mass.) and as reviewed in reference [33].
  • potential binding compounds may be designed as a whole or “de novo” using either an empty active site or, optionally, including some portion(s) of a known inhibitor(s), activator(s) or stabilizer (s).
  • Suitable computer programs include, but are not limited to, LUDI [34], LEGEND [35]; and LEAPFROG (Tripos Associates, St. Louis, Mo.). Other molecular modeling techniques may also be employed in accordance with this invention [36,37].
  • a potential binding compound has been designed, selected, identified, synthesized, or chosen by the methods described herein, the affinity with which that compound binds to FAPP2 (and/or GLTP) may be tested and optimized by computational evaluation.
  • a compound designed, or selected, or synthesized, or chosen as potential binding compound or may be further computationally optimized so that in its bound state it would preferably lack repulsive electrostatic interaction with the target site.
  • Such non-complementary (e.g., electrostatic) interactions include repulsive charge-charge, dipole-dipole and charge-dipole interactions.
  • Suitable computer software which may be used to evaluate compound deformation energy and electrostatic interactions, includes, but is not limited to, Gaussian 92, revision C by M. J. Frisch, Gaussian, Inc., (1992) Pittsburgh, Pa.; AMBER, version 4.0 by P. A. Kollman, (1994) University of California at San Francisco; QUANTA/CHARMM by Molecular Simulations, Inc., (1994) Burlington, Mass.; and Insight II/Discover by Biosysm Technologies Inc., (1994) San Diego, Calif.
  • binding compounds may be specifically designed and/or selected and/or synthesized and/or chosen by the above methods to induce non-complementary (e.g., electrostatic) interactions, such as repulsive charge-charge, dipole-dipole and charge-dipole interactions.
  • non-complementary interactions such as repulsive charge-charge, dipole-dipole and charge-dipole interactions.
  • the sum of all electrostatic interactions between the potential binding compound and the site at which it is bound to FAPP2 make a contribution to the enthalpy of binding that is not neutral.
  • the above method comprises using a suitable computer program in designing and/or selecting a potential binding compound.
  • the above methods comprise using a suitable computer program in conjunction with synthesizing and/or choosing the potential binding compound.
  • the above method further comprises the steps of using a suitable assay, as described herein, to characterize the potential binding compound's ability to bind to FAPP2 (and/or GLTP). This may involve directly testing the compound's ability to bind, and/or determining whether the compound has an influence on FAPP2 activity (e.g. by affecting its transfer activity, stability, folding, and/or intracellular localization).
  • assays may be used, such as, calorimetric techniques (e.g. isothermal titration calometry, differential scanning calometry), or BiacoreTM.
  • calorimetric techniques e.g. isothermal titration calometry, differential scanning calometry
  • BiacoreTM BiacoreTM
  • the above methods may further comprise determining whether the potential binding compound modulates the activity (e.g. transfer activity), stability or intracellular trafficking of FAPP2 (and/or GLTP). This may be carried out using a biological assay.
  • Determining whether the potential binding compound modulates the transfer activity of FAPP2 may involve contacting the potential binding compound with FAPP2 in the presence of a substrate (e.g. GlcCer) and determining the amount of substrate transfer. This can be compared to the amount of substrate transfer in the absence of the potential binding compound to determine the effect of the potential binding compound on FAPP2 transfer activity. Suitable assays for FAPP2 are known in the art and discussed above.
  • Determining whether the potential binding compound modulates the stability of FAPP2 (and/or GLTP) may involve e.g. differential scanning calorimetry (DSC), circular dichroism (CD) spectra analyses.
  • DSC differential scanning calorimetry
  • CD circular dichroism
  • Determining whether the potential binding compound modulates the intracellular trafficking of FAPP2 (and/or GLTP) may involve cell based assays.
  • the methods of the invention may further comprise the step of modifying the binding compound for administration as a pharmaceutical.
  • the binding compound may have the required ability to bind to FAPP2 (and/or GLTP), as discussed above, but may still benefit from further optimisation.
  • the binding compound's chemical structure is used as a starting point for chemical modifications. Such modifications may be designed to improve potency, selectivity, pharmacokinetic parameters or physicochemical properties (e.g. stability, solubility).
  • the methods of the invention may further comprise the step of formulating the binding compound, or the modified binding compound as a pharmaceutical.
  • This will in general involve admixing the agent with a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier includes any agent that does not itself induce toxicity effects or cause the production of antibodies that are harmful to the individual receiving the pharmaceutical composition.
  • Pharmaceutically acceptable carriers may additionally contain liquids such as water, saline, glycerol, ethanol or auxiliary substances such as wetting or emulsifying agents, pH buffering substances and the like.
  • the pharmaceutical carrier employed will thus vary depending on the route of administration. Carriers may enable the pharmaceutical compositions to be formulated into tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions to aid intake by the patient. A thorough discussion of pharmaceutically acceptable carriers is available in [38].
  • the invention provides computer readable media comprising the atomic coordinates for the polypeptide of the invention, or a subset thereof.
  • the computer readable medium may further comprise programming for displaying a molecular model of the polypeptide or a portion thereof.
  • the computer readable medium may further comprise programming for identifying a binding molecule and to assist with this it may further comprise a database of structures of test compounds.
  • test compounds may, for example be based on known inhibitors of FAPP2 and may for example be analogues of GlcCer.
  • the said atomic coordinates are set forth in Tables 1 to 3.
  • Computer readable media refers to any media which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media such as floppy discs, hard disc storage medium and magnetic tape; optical storage media such as optical discs or CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media.
  • a computer comprising the computer-readable medium of the invention is provided, as is a computer system comprising a memory unit comprising x-ray crystallographic structure coordinates defining the polypeptide of the invention as set forth in Table 1, or a subset thereof; and a processor in electrical communication with the memory unit; wherein the processor generates a molecular model having a three dimensional structure representative of at least a portion of said polypeptide.
  • a “computer system” refers to the hardware means, software means and data storage means used to analyse the atomic coordinate data of the present invention.
  • the minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means and data storage means. Desirably a monitor is provided to visualise structure data.
  • the data storage means may be RAM or means for accessing computer readable media of the invention. Examples of such systems are microcomputer workstations available from Silicon Graphics Incorporated and Sun Microsystems running Unix based, Windows.
  • a compound identified, designed, selected and/or optimised by a method of the invention is provided in a further aspect of the invention, as are such compounds which have been modified for administration as a pharmaceutical, and/or which have been formulated as a pharmaceutical.
  • Such compounds may be used as a medicament, e.g. in treating Fabry's disease.
  • Methods of treating or preventing Fabry's disease comprising administering an effective amount of such a compound or pharmaceutical to a patient in need thereof are furthermore provided.
  • a further aspect of the invention provides a method of producing a pharmaceutical composition comprising designing, selecting and/or optimising a compound with the methods of the invention, modifying the identified compound for administration as a pharmaceutical and formulating the product obtained with a pharmaceutically acceptable carrier or diluent.
  • Any pharmaceutical may be delivered by any known route of administration.
  • the pharmaceutical may be delivered locally or systemically. It may be delivered by a parenteral route (e.g. by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue), or into a lesion.
  • parenteral route e.g. by injection, either subcutaneously, intraperitoneally, intravenously or intramuscularly or delivered to the interstitial space of a tissue
  • Other modes of administration include oral and pulmonary administration, suppositories, and transdermal or transcutaneous applications, needles, and hyposprays.
  • the pharmaceutical may be administered alone or as part of a treatment regimen also involving the administration of other drugs currently used in the treatment of patients with Fabry disease.
  • it may be administered in combination with enzyme replacement therapy or with treatments associated with the treatment of the clinical manifestations of the disease, such as analgesics, anticonvulsants, and non-steroidal anti-inflammatory drugs (NSAIDs).
  • NSAIDs non-steroidal anti-inflammatory drugs
  • the agent may be administered simultaneously, sequentially or separately with the other drug(s).
  • the agent may be administered before or after administration of the other drug(s).
  • FIG. 1 Two molecules of T4L-FAPP2-C212 in crystallographic AU (Mol-A and Mol-B in cyan and green respectively)
  • FIG. 2 Two adjacent T4L-FAPP2-C212 molecules in crystal lattice, showing extensive interaction between T4L
  • FIG. 3 18:1 Glucosyl Ceramide (GlcCer, shown in green sticks) is docked into the structure of FAPP2-C212, without further energy minimization. Coordinates of GlcCer was taken from PDB ID: 3S0K. Hydrophobic residues of FAPP2 in close proximity of oleoyl and sphingosine chains are shown in stick model. Residues making contacts with glucosyl head group are shown in stick model and are labeled.
  • FIG. 4 Electron density map around W407 is shown here with docked 18:1 GlcCer (see FIG. 3 ). No energy minimization was done after docking.
  • FIG. 5 T4L-FAPP2-C212 crystals.
  • FIG. 6 FAPP2-C212 structure (T4L has been removed for clarity) (a) with hGLTP for comparison (b).
  • FIG. 7 Sugar head group binding: FAPP2-C212 (apo) versus hGLTP complex (PDB: 4H2Z).
  • FAPP2 is shown in green and GLTP in cyan.
  • Monosulfo-Galactosyl Ceramide bound to hGLTP is shown in pink.
  • FIG. 8 FFAT-like motif in FAPP2 and GLTP (PDB ID: 2EUK).
  • the FFAT motif (two Phe in acidic track) interacts with VAP proteins (vesicle-associated membrane protein associated proteins).
  • F311 of FAPP2 and F33 of hGLTP take the same place (at the tail of ceramide 24:1).
  • FAPP2 is shown in cyan and hGLTP in green.
  • the 24:1 Galactosylceramide bound to hGLTP is in orange.
  • the FFAT FAPP2-like motif is potentially involved in stability of the GLTP fold and ceramide release.
  • FAPP2-C212 C-terminal 212 amino acids, aa 308-519, of FAPP2 (FAPP2-C212) was expressed as SUMO or His fusions and purified as fusion proteins or as tag removed FAPP2-C212. These proteins were concentrated to 6-16 mg/ml for crystallization studies. Crystallization screening was carried out with purified FAPP2-C212 molecules using commercial crystallization screening kits from Qiagen (JCSG kits I-IV) by sitting drop vapour diffusion method. Crystallization screening was also carried out for FAPP2-C212 incubated with various ligands that are known to bind to FAPP2 or human GLTP proteins, including C8-ceramide, Phlorizin, disulfo or monosulfo galactosyl ceramides. These crystallization trials did not yield any promising crystallization hit.
  • lysozyme T4L was chosen, as crystallisable fusion tag, to facilitate crystallization.
  • T4L-FAPP2-C212 His-T4L-FAPP2-C212 (T4L-FAPP2-C212) was cloned into pRSET vector (Life Technologies), expressed in E. coli and purified by Ni-column and SEC column processes. Purified protein has a molecular weight of 47.2 kDa. T4L-FAPP2-C212 was concentrated to 6 mg/ml and crystallization trial was carried out using JCSG-I random matrix crystallization kit from Qiagen. All crystallization experiments were carried by sitting drop vapour diffusion method in 16° C. incubators. Initial crystallization hit was observed in condition# C6 JCSG kit-1 after three days.
  • T4L-FAPP2-C212 T4L structure (PDB ID: 3G3V) and hGLTP structure (PDB ID: 1SWX) were used as search models. Molrep was used for MR, refmac5 was used for refinement and coot for used for model building.
  • T4L-FAPP2-C212 There are two molecules of T4L-FAPP2-C212 in the asymmetric unit, referred as Mol-A and Mol-B ( FIG. 1 ). T4L from adjacent molecules in the crystal lattice make extensive contacts that appear to have facilitated crystallization ( FIG. 2 ). In the electron density map, aa 308-514 of FAPP2 for molecule-A and 308-515 of FAPP2 for molecule-B could be seen, without ambiguity. Electron densities are not clear for side chains of K190, 1322, E326, 5328, E333 and E509 of molecule-A and K190, L324, L325, E326, K377, E378 and R398 of molecule-B
  • Residues involved ceramide binding including W407, H445, D360 and other hydrophobic residues that interact with acyl sphingosine chains of ceramide are well refined in the electron density map.
  • Glucosylceramide containing oleoyl acyl chain (18:1) from PDB ID: 3S0K was docked into the ligand binding pocket of our current FAPP2 structure ( FIG. 3 ) and the corresponding electron density map is shown in FIG. 4 . No energy minimization was done after docking.
  • FIG. 6 shows the FAPP2-C212 structure, compared to that of hGLTP (PDB ID 1SWX).
  • the sugar headgroup binding residues of FAPP-C212 were compared to those of the hGLTP complex with monosulfo-galactosyl ceramide (PDB ID 4H2Z). It was observed that there is more negative charge near to the sugar headgroup in FAPP2, and further in FAPP2 the K367 is positioned and the positively charged loop around R398 is projected by a hydrogen bond between K367 and N399 ( FIG. 7 ).
  • REMARK 3 PROGRAM REFMAC 5.8.0071 REMARK 3 AUTHORS: MURSHUDOV, SKUBAK, LEBEDEV, PANNU, REMARK 3 STEINER, NICHOLLS, WINN, LONG, VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET: MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT.
  • REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS): 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS): 88.73 REMARK 3 DATA CUTOFF (SIGMA (F)): NONE REMARK 3 COMPLETENESS FOR RANGE (%): 99.37 REMARK 3 NUMBER OF REFLECTIONS: 34535 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.
  • REMARK 3 CROSS-VALIDATION METHOD THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION: RANDOM REMARK 3 R VALUE (WORKING + TEST SET): 0.20798 REMARK 3 R VALUE (WORKING SET): 0.20541 REMARK 3 FREE R VALUE: 0.25742 REMARK 3 FREE R VALUE TEST SET SIZE (%): 4.9 REMARK 3 FREE R VALUE TEST SET COUNT: 1782 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
  • REMARK 3 ALL ATOMS 6104 REMARK 3 REMARK 3 B VALUES.

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